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SRX8651878: ddRADseq of Aichryson bituminosum
1 ILLUMINA (Illumina MiSeq) run: 239,408 spots, 137.9M bases, 67.1Mb downloads

Design: The restriction enzymes BamHI and KpnI were used for digestion. The library was size selected to 350-720 bp using Pippin Prep and sequenced using the Illumina MiSeq v3 kit for 300 bp PE reads.
Submitted by: Johannes Gutenberg University
Study: Double Digest RADseq for Long Loci (llddRADseq)
show Abstracthide Abstract
Restriction-site associated DNA sequencing (RADseq) is becoming popular in evolutionary and phylogenetic studies fostered by the relatively simple, fast and cost-effective data acquisition in non-model organisms. However, using this type of genomic data to resolve phylogenetic relationships among closely related species is hampered by missing data, difficulties in locus assembly and a low number of phylogenetically informative sites per locus. Here we test whether a modified ddRADseq protocol, which includes a pre- and a post-amplification size selection step to reduce the locus pool from tens of thousands to several thousand with a fixed length of 300-600bp, has the potential to generate a RAD dataset variable enough for resolving rapid radiations by incorporating coalescent-based summary methods in addition to widely used concatenated-based maximum likelihood approaches. Furthermore, we demonstrate how to assemble such long RAD fragments using the ipyrad pipeline and a customized clustering optimization approach, and give guidance for generatingfiltered datasets for a comparative phylogenetic analysis with RAxML, ASTRAL III, SVDquartets and IQ-TREE. Using the plant genus Aichryson (Crassulaceae) as an example, we show that the long and variable loci dataset, generated by utilization of an optimized assembly/clustering and dataset filtering approach, supports maximum likelihood methods as well as coalescent-based summary methods for phylogenetic tree reconstructions. These are further evaluated with respect to gene- and site concordance factors using IQ-TREE, which in combination are able to reveal a complex phylogenetic history. We conclude that our llddRADseq approach is a powerful and efficient tool for phylogenomics especially in species-rich, non-model lineages.
Sample:
SAMN15402400 • SRS6935286 • All experiments • All runs
Library:
Name: A02_J03
Instrument: Illumina MiSeq
Strategy: RAD-Seq
Source: GENOMIC
Selection: Restriction Digest
Layout: PAIRED
Runs: 1 run, 239,408 spots, 137.9M bases, 67.1Mb
Run# of Spots# of BasesSizePublished
SRR12130693239,408137.9M67.1Mb2020-07-02

ID:
11250758

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